Citations

Abstract Motivation Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. Results We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric—fitness diversity—which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. Availability and implementation R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

Abstract Background Stroke is a leading cause of mortality and disability globally. However, information about stroke burden in the Philippines is limited. We sought to analyze stroke burden in the Philippines from 1990 to 2023. Methods Incidence, prevalence, mortality, and disability-adjusted life-years (DALYs) estimates from the Global Burden of Disease Study 2023 data were used as indicators to analyze the burden of stroke by sex and age. Temporal trends in both crude and age-standardized rates were analyzed using joinpoint regression analysis. Results In 2023, stroke incidence was estimated at 156.2 (95% uncertainty interval [UI]: 140.8–175.4) thousand, prevalence at 1.2 (95% UI: 1.2–1.4) million, mortality at 72.2 (95% UI: 63.2–83.0) thousand, and DALYs at 2.1 (95% UI: 1.8–2.3) million. High systolic blood pressure was the leading contributor to risk-attributable stroke mortality and DALYs. Since 1990, age-standardized rates declined significantly, whereas crude rates increased markedly. Compared with women, men had a higher fatal burden and consistently exhibited a higher age-standardized burden. Although older adults (≥ 55 years) had the highest stroke burden and achieved reductions in stroke incidence and fatal outcomes, both fatal and non-fatal burdens consistently increased among young adults (35–54 years). Conclusion While age-standardized rates have improved, the rising crude burden and shift towards younger adults present significant public health challenges. These trends highlight the pressing need for aggressive and targeted risk factor control, sustained risk monitoring, and strengthened acute and post-stroke care to mitigate the growing health burden of stroke in the Philippines.

Abstract Introduction: DRd is the standard of care for frontline (FL) treatment (tx) of transplant-ineligible (TIE) patients with newly diagnosed multiple myeloma (NDMM). This is supported by its superior efficacy and tolerable safety profile vs lenalidomide and dexamethasone (Rd) and vs bortezomib plus Rd (VRd) per the phase 3 MAIA clinical trial and real-world data. However, based on recent phase 3 CEPHEUS and IMROZ trial data, the tx paradigm is shifting toward the use of quadruplets for suitable TIE patients with NDMM. CEPHEUS demonstrated the superior efficacy of DVRd vs VRd in TIE and transplant-deferred patients with NDMM. DVRd-treated patients achieved significantly higher rates of minimal residual disease negativity and significantly improved progression-free survival vs VRd-treated patients. DVRd is listed as a National Comprehensive Cancer Network (NCCN) Category 1 preferred regimen in this setting and is therefore used in US real-world clinical practice. The objective of this study was to evaluate real-world usage patterns of FL DVRd and FL DRd in nontransplanted patients with NDMM and to assess the characteristics of patients treated with these regimens. Methods:Data from the Flatiron Health Research database were used for this retrospective observational study. Patients were included in this analysis if they received FL tx with DVRd or DRd for NDMM between Jan 1, 2019, and Dec 31, 2024. The index date was defined as the initiation date of FL DVRd or FL DRd. As the Flatiron database does not capture transplant eligibility status, the analysis excluded all patients who underwent hematopoietic stem cell transplantation at any time during the study period. Patients were also excluded if they were <18 years of age, enrolled in a clinical trial, had presence of other cancers, received chimeric antigen receptor T-cell therapy, or were diagnosed with amyloid light-chain amyloidosis before the index date. High cytogenetic risk was defined as the presence of abnormalities including del(17p), t(4;14), or t(14;16). Descriptive statistics were used to report demographic and clinical characteristics. Kaplan-Meier methods were used to estimate duration of therapy. Results: Among the nontransplanted NDMM cohort, 704 FL DVRd-treated patients and 396 FL DRd-treated patients were identified. At index, FL DVRd patients were generally younger than FL DRd patients (median age, 68 vs 78 years, respectively), more likely to be male (55.3% vs 49.5%), and less likely to have Medicare coverage (8.4% vs 17.2%). The 2 cohorts had similar proportions of Black/African American patients (18.9% and 18.7%). Among patients with available data, high cytogenetic risk was more frequently observed in FL DVRd (29.2%) vs FL DRd (17.5%) patients; a lower proportion of FL DVRd patients had International Staging System (ISS) stage III disease (27.1%) than ISS stage I disease (39.9%), whereas a higher proportion of FL DRd patients had ISS stage III disease (32.9%) than ISS stage I disease (25.5%). FL DVRd patients were more likely to be nonfrail (Intergroupe Francophone du Myélome simplified frailty score <2) vs FL DRd patients (64.6% vs 28.2%). Use of both DVRd and DRd increased during the study period; however, the increase was greater for DVRd, particularly in the later years. Notably, FL DVRd was started in 10 patients in 2019, increasing to 146 in 2022 and 222 in 2024. By comparison, FL DRd was initiated in 17 patients in 2019, increasing to 85 in 2022 and 97 in 2024. Median follow-up was 15.6 mo in the DVRd cohort and 20.3 mo in the DRd cohort. Median duration of DVRd therapy was 18.5 mo (95% CI, 14.8–22.7) and was 23.5 mo (95% CI, 19.0–31.7) for DRd therapy. Bortezomib as part of the DVRd regimen was given once weekly or less frequently in the majority (65.6%) of patients. Conclusions: These real-world data show the increasing FL use of the daratumumab-based quadruplet regimen DVRd among nontransplanted patients with NDMM. FL DVRd patients were generally younger and less frail but more likely to have high cytogenetic risk than those treated with DRd. These data also show that daratumumab-based regimens, either as a triplet (DRd) or a quadruplet (DVRd), are increasingly adopted over time in real-world clinical practice. These data further suggest that DRd and DVRd may be considered foundational for the tx of nontransplanted patients with NDMM regardless of patient characteristics, including age, frailty, cytogenetic risk, and ISS stage.

ABSTRACT Intratumor heterogeneity arises from ongoing somatic evolution complicating cancer diagnosis, prognosis, and treatment. Here we present TEATIME (es t imating e volution a ry events t hrough s i ngle-ti m epoint s e quencing), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric—fitness diversity—which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types.

Abstract Purpose: Germline alterations in homologous recombination repair (gHRR) genes affect the pathogenesis, treatment options, and survival of patients with cancer. However, distinct gHRR gene alterations may differentially affect treatment response and oncogenic signaling. In this study, we interrogated genomic and transcriptomic data and assessed clinical outcomes of patients with gHRR mutations across four BRCA-associated cancers (breast, ovarian, pancreatic, and prostate cancers) to identify therapeutic vulnerabilities. Experimental Design: We assessed 24,309 patients undergoing matched tumor/normal next-generation DNA and RNA sequencing. Annotated gHRR gene variants [germline BRCA1, germline BRCA2, germline PALB2, germline ATM (gATM), and germline CHEK2] were analyzed. HRs were used to assess survival outcomes comparing germline versus sporadic groups. Somatic alterations and their frequencies were compared across gHRR-altered groups. Differential gene expression and gene set enrichment analysis were used to compare transcriptomic profiles. Results: Somatic TP53 mutations were depleted in gATM carriers (P < 0.05) across all four BRCA-associated cancers by up to 2.5-fold. Tumors with germline BRCA1/2 mutations were associated with improved survival in patients with ovarian cancer and had consistent enrichment of TP53 mutations in all four cancers. gATM mutations displayed elevated p53 transcriptional activity in all four cancers, with significance reached in breast and prostate cancers (P < 0.01). In breast, ovarian, and prostate cancers, gATM tumors demonstrated significantly increased inflammatory pathways (P < 0.001). Finally, using gene dependency data, we found that cell lines that were highly dependent on ATM were co-dependent on canonical p53 function. Conclusions: gATM-associated cancers seem to require intact p53 activity and this synthetic essentiality may be used to guide targeted therapies that perturb canonical TP53 function.

Abstract Background Agricultural contaminants, including inhaled organic dust (OD) and gases, are known to cause inflammation in the lungs and the brain. We investigated the role of the potassium channel Kv1.3 in organic dust (OD)-induced neuroinflammation models. Kv1.3 channels play a multifaceted role in microglial immune modulation, cancer, neurodegenerative diseases, and constitute a potential therapeutic target. Methods We used in vivo (C57BL/6 mice), in vitro (microglial cell line, primary microglia), and ex vivo (brain slice culture) models of OD-induced neuroinflammation. A sterile OD extract (ODE) was prepared, and mice were exposed to either normal saline or ODE intra-nasally for 5 weeks (5 days/week) to simulate an occupational exposure scenario. Primary microglia were isolated from neonatal mice for total RNA sequencing (RNA-seq). The ODE-induced expression of Kv1.3 was quantified using in vitro and ex vivo models with and without PAP-1 treatments. Exposure-induced changes in cytokines and reactive species markers were measured. Using western blot, we quantified phosphorylated p38 MAPK14 (p-p38 MAPK) and NOX2. We measured the currents through Kv1.3 channels using a microglial patch-clamp assay. Results Exposure to ODE increased the expression of Kv1.3 and p-p38 MAPK in mouse microglia without affecting the Kv1.3 currents at the cell surface. Exposure increased the levels of inflammatory cytokines and NOX2. Kv1.3 inhibition with PAP-1 decreased inflammatory markers (TNF-α and IL-6), levels of Kv1.3, p-p38 MAPK, NOX2, and nitrites. Conclusion Our study revealed that pharmacological inhibition of Kv1.3 potassium channels reduces ODE-induced neuroinflammation by decreasing inflammatory and oxidative stress markers.

Background and Aims: Biliary tract cancers (BTCs), including intrahepatic cholangiocarcinoma (iCCA), extrahepatic cholangiocarcinoma, gallbladder cancer, and ampullary cancer, exhibit poor prognosis. This study examined temporal trends in mortality due to BTCs and their major subtypes at international, regional, and national levels. Approach and Results: This observational study used the World Health Organization mortality database. Locally weighted regression (LOESS) was used to produce a smoothed curve of long-term international and regional BTC and major subtype-related mortality rates in 2000–2022 based on available data from countries. Trends in age-standardized mortality rates (ASRs) during 2013–2022 for individual countries were examined using joinpoint regression analysis. Internationally, LOESS-smoothed ASRs per 100,000 population due to BTCs were 2.8 (95% CI: 2.5–3.1) in 2000, and 2.7 (2.3–3.1) in 2022. LOESS-smoothed BTC-related ASRs were the highest in the Western Pacific region at 4.2 (1.8–6.6) in 2022, compared with those in the European and American regions at 2.6 (2.3–2.9) and 2.2 (1.8–2.6), respectively. Among major subtypes, LOESS-smoothed ASRs due to iCCA increased by 120.0%, those due to gallbladder cancer decreased by 45.5%, and those due to extrahepatic cholangiocarcinoma remained stable between 2000 and 2022. Disparities in BTC and major subtype-related ASR trends were observed between countries during 2013–2022, with iCCA-associated ASRs showing increasing trends in many countries. Conclusions: Although internationally estimated BTC-associated ASRs showed a stable trend over the last 2 decades, a large increase in estimated iCCA-associated ASRs necessitates developing effective screening for high-risk individuals and disease management strategies.

Abstract Extracellular vesicles (EVs) are small membrane‐bound structures that originate from various cell types and carry molecular cargos to influence the behaviour of recipient cells. The use of EVs as biomarkers for diagnosis and as delivery vehicles for treatment in a wide range of human disease is a rapidly growing field in research and clinical practice. We hypothesized that electric fields (EFs) could influence the release and content of EVs. To examine this hypothesis, we developed a specialized bioreactor enabling cells to thrive in a three‐dimensional setting, replicating in‐vivo conditions amidst programmable EF environments. We established a three‐step EV purification protocol to achieve high‐density production of EVs. We also performed mass spectrometry‐based proteomics analysis on EV‐carrying proteins and used high‐resolution nanoparticle flowcytometry for single‐vesicle analysis. Findings from this report suggest that electrical stimulation, employing physiologically relevant amplitudes typical in therapeutic deep brain stimulation, influences the release of EVs and their cargo content in a frequency‐dependent fashion. This conclusion could carry significant implications for both fundamental biological understanding and medical advancements. First, it raises an intriguing question about how the endogenous electrical activity of neuronal and other cellular assemblies influence the production and composition of EVs. Second, it reveals a novel underlying mechanism of how therapeutic electrical stimulations can modulate EVs and treat human brain disorders. Third, it provides a novel approach to utilize electrical stimulation for generating desired EV cargos in a programmable setting.